|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectuk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
public class GFMerge_Analysis
class which wraps analysis of gene predictions
Gene predicter, prediction, genemodel region, cDNA region, Blast region objects are created within the class.
An region array of picked gene models is returned.
GFMergeRegion
,
GeneModel
,
Prediction
Field Summary | |
---|---|
private static int |
_aminoacidsLength
|
private SimpleArg |
allArguments
object which contains all command line parameters |
private java.util.ArrayList |
analysisObjArr
ArrayList which contains analysis objects ( CDnaSpliceSiteAnalysis , CDnaOverlapAnalysis , BlastOverlapAnalysis , TotalExonLengthAnalysis , GeneModelLengthAnalysis , AvgCondProbAnalysis ) |
private java.util.ArrayList |
arrListOfBlastRegions
ArrayList of Blast regions |
private java.util.ArrayList |
arrListOfCDnaRegions
ArrayList of cDNA regions |
private java.util.ArrayList |
arrListOfGMRegions
ArrayList of genemodels from which low scoring genemodels are removed during analysis |
private java.util.ArrayList |
arrListOfGMRegions_org
ArrayList of genemodel regions which contains all of the original gene models |
private java.util.ArrayList |
genePredicters
ArrayList of gene predicter objects |
private java.util.ArrayList |
mergedFeatureTableArr
return value of getMergedFeatureTable, contains regions of picked genemodels |
private java.util.ArrayList |
predictions
ArrayList of prediction objects |
Constructor Summary | |
---|---|
GFMerge_Analysis(SimpleArg _allArguments)
constructor of GFMerge_Analysis objects |
Method Summary | |
---|---|
private static java.util.ArrayList |
calcArrListOfBlastRegions(SimpleArg _allArguments)
method which creates ArrayList of Blast regions |
private static java.util.ArrayList |
calcArrListOfCDnaRegions(SimpleArg _allArguments)
method which creates ArrayList of cDNA regions |
private static java.util.ArrayList |
calcArrListOfGMRegions(java.util.ArrayList _predictions,
SimpleArg _allArguments)
method which calulates prediction objects |
private java.util.ArrayList |
calcMergedFeatureTable()
method which is called from getMergedFeatureTable if variable mergedFeatureTableArr is null . |
private static java.util.ArrayList |
copyArrOfFeatRegions(java.util.ArrayList arrListOfFeatRegions)
method which does a deep copy of an region array, it keeps the references to the genemodel objects |
private void |
countFeat(java.util.ArrayList ArrListOfRegions)
|
private java.util.ArrayList |
createAnalysisObjArr(java.util.ArrayList _arrListOfGMRegions,
java.util.ArrayList _arrListOfCDnaRegions,
java.util.ArrayList _arrListOfBlastRegions,
SimpleArg _allArguments)
method which generated an ArrayList of analysis objects ( CDnaSpliceSiteAnalysis , CDnaOverlapAnalysis , BlastOverlapAnalysis , TotalExonLengthAnalysis , GeneModelLengthAnalysis , AvgCondProbAnalysis ) |
private static java.util.ArrayList |
createGeneFinderObjects(SimpleArg _allArguments)
methode which creates genefinder objects and calculates their accuracy |
private static java.util.ArrayList |
createPredictionObjects(SimpleArg _allArguments,
java.util.ArrayList _genePredicters)
method which creates Prediction objects |
private static MyTreeMap |
createSimFeatObjects(java.lang.String featFilename,
MyTreeMap _allFeatTreeMap)
method which creates similarity feature objects (cDNA, Blast), puts them in a MyTreeMap object and returns this tree map |
private static MyTreeMap |
createTreeOfGMs(java.util.ArrayList _predictions,
MyTreeMap _allGmTreeMap)
method which creates a tree structure of genemodels which are sorted by their minimum location |
private SimpleArg |
getAllArguments()
accessor method which returns the object containg all command line parameters |
private java.util.ArrayList |
getAnalysisObjArr()
accessor method which returns ArrayList of analysis objects generated in calcAnalysisObjArr ( CDnaSpliceSiteAnalysis , CDnaOverlapAnalysis , BlastOverlapAnalysis , TotalExonLengthAnalysis , GeneModelLengthAnalysis , AvgCondProbAnalysis ) |
private java.util.ArrayList |
getArrListOfBlastRegions()
accessor method which return ArrayList of Blast regions |
private java.util.ArrayList |
getArrListOfCDnaRegions()
accessor method which returns ArrayList of cDNA regions |
java.util.ArrayList |
getArrListOfGMRegions_org()
accessor method which returns an array list of regions which correspond to the original array used in the constructor |
java.util.ArrayList |
getArrListOfGMRegions()
accessor method which returns ArrayList of genemodel regions |
java.util.ArrayList |
getMergedFeatureTable()
method which returns an array list of regions only containing the genemodels which have been picked during the process of scoring |
java.util.ArrayList |
getPredictions()
accessor method which returns an array list of prediction objects |
private static org.biojava.bio.seq.Sequence |
removeNonCdsFeatures(org.biojava.bio.seq.Sequence sequence,
int _aminoacidsLength)
method which removes non-CDS features from sequence |
private void |
setAllArguments(SimpleArg _allArguments)
accessor method which sets SimpleArg object containing all command line parameters |
private void |
setAnalysisObjArr(java.util.ArrayList _analysisObjArr)
accessor method which sets ArrayList of analysis objects generated in calcAnalysisObjArr ( CDnaSpliceSiteAnalysis , CDnaOverlapAnalysis , BlastOverlapAnalysis , TotalExonLengthAnalysis , GeneModelLengthAnalysis , AvgCondProbAnalysis ) |
private void |
setArrListOfBlastRegions(java.util.ArrayList _arrListOfBlastRegions)
accessor method which sets ArrayList of Blast regions |
private void |
setArrListOfCDnaRegions(java.util.ArrayList _arrListOfCDnaRegions)
accessor method which sets ArrayList of cDNA regions |
private void |
setArrListOfGMRegions_org(java.util.ArrayList _arrListOfGMRegions_org)
accessor method which sets ArrayList of original genemodel regions |
private void |
setArrListOfGMRegions(java.util.ArrayList _arrListOfGMRegions)
accessor method which sets ArrayList of genemodel regions |
private void |
setGenePredicters(java.util.ArrayList _genePredicters)
accessor method which sets ArrayList of genepredicter objects |
private void |
setMergedFeatureTableArr(java.util.ArrayList _mergedFeatureTableArr)
accessor method which sets mergedFeatureTableArr with ArrayList of regions which contain high scoring genemodels |
private void |
setPredictions(java.util.ArrayList _predictions)
accessor method which sets ArrayList of prediction objects |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
private java.util.ArrayList genePredicters
private java.util.ArrayList predictions
private java.util.ArrayList arrListOfGMRegions_org
private java.util.ArrayList arrListOfGMRegions
private java.util.ArrayList arrListOfCDnaRegions
private java.util.ArrayList arrListOfBlastRegions
private java.util.ArrayList analysisObjArr
CDnaSpliceSiteAnalysis
, CDnaOverlapAnalysis
, BlastOverlapAnalysis
, TotalExonLengthAnalysis
, GeneModelLengthAnalysis
, AvgCondProbAnalysis
)
private java.util.ArrayList mergedFeatureTableArr
private SimpleArg allArguments
private static int _aminoacidsLength
Constructor Detail |
---|
public GFMerge_Analysis(SimpleArg _allArguments)
It takes a SimpleArg object as parameter which contains itself all command line arguments.
_allArguments
- objectSimpleArg
Method Detail |
---|
public java.util.ArrayList getMergedFeatureTable()
There should be no overlapping gene models anymore.
ArrayList
of regionsGFMergeRegion
,
GeneModel
private void countFeat(java.util.ArrayList ArrListOfRegions)
private java.util.ArrayList calcMergedFeatureTable()
mergedFeatureTableArr
is null
. It calculates the high scoring genemodels which are picked during analysis.
private java.util.ArrayList createAnalysisObjArr(java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfCDnaRegions, java.util.ArrayList _arrListOfBlastRegions, SimpleArg _allArguments)
CDnaSpliceSiteAnalysis
, CDnaOverlapAnalysis
, BlastOverlapAnalysis
, TotalExonLengthAnalysis
, GeneModelLengthAnalysis
, AvgCondProbAnalysis
)
_arrListOfGMRegions
- ArrayList which contains region of genemodels_arrListOfCDnaRegions
- ArrayList which contains region of cDNA
objects_arrListOfBlastRegions
- ArrayList which contains region of
Blast objects_allArguments
- object which contains all command line
arguments
BasicFeatureAnalysis
)public java.util.ArrayList getArrListOfGMRegions_org()
ArrayList
of regionsGFMergeRegion
,
GeneModel
public java.util.ArrayList getPredictions()
ArrayList
of predictionsPrediction
private static java.util.ArrayList copyArrOfFeatRegions(java.util.ArrayList arrListOfFeatRegions)
arrListOfFeatRegions
- ArrayList of feature regions (cDNA, Blast)
private static java.util.ArrayList createGeneFinderObjects(SimpleArg _allArguments)
_allArguments
- object which contains all command line arguments
private static java.util.ArrayList createPredictionObjects(SimpleArg _allArguments, java.util.ArrayList _genePredicters)
Prediction
objects
_allArguments
- object which contains all command line arguments_genePredicters
- ArrayList which contains all genepredicters
private static org.biojava.bio.seq.Sequence removeNonCdsFeatures(org.biojava.bio.seq.Sequence sequence, int _aminoacidsLength)
sequence
- BioJava sequence object
private static java.util.ArrayList calcArrListOfGMRegions(java.util.ArrayList _predictions, SimpleArg _allArguments)
_predictions
- ArrayList which contains all prediction objects_allArguments
- object which contains all command line
arguments
private static MyTreeMap createTreeOfGMs(java.util.ArrayList _predictions, MyTreeMap _allGmTreeMap)
_predictions
- ArrayList which contains all prediction objects_allGmTreeMap
- empty MyTreeMap which will contain the return
value
private static java.util.ArrayList calcArrListOfCDnaRegions(SimpleArg _allArguments)
_allArguments
- object which contains all command line arguments
private static java.util.ArrayList calcArrListOfBlastRegions(SimpleArg _allArguments)
_allArguments
- object which contains all command line arguments
private static MyTreeMap createSimFeatObjects(java.lang.String featFilename, MyTreeMap _allFeatTreeMap)
featFilename
- filename of the embl file which contains features_allFeatTreeMap
- empty MyTreeMap which will contain the return
value
public java.util.ArrayList getArrListOfGMRegions()
private java.util.ArrayList getArrListOfCDnaRegions()
private java.util.ArrayList getArrListOfBlastRegions()
private java.util.ArrayList getAnalysisObjArr()
CDnaSpliceSiteAnalysis
, CDnaOverlapAnalysis
, BlastOverlapAnalysis
, TotalExonLengthAnalysis
, GeneModelLengthAnalysis
, AvgCondProbAnalysis
)
private SimpleArg getAllArguments()
private void setArrListOfGMRegions(java.util.ArrayList _arrListOfGMRegions)
_arrListOfGMRegions
- ArrayList which contains region of genemodel
objectsprivate void setArrListOfCDnaRegions(java.util.ArrayList _arrListOfCDnaRegions)
_arrListOfCDnaRegions
- ArrayList of feature cDNA regionsprivate void setArrListOfBlastRegions(java.util.ArrayList _arrListOfBlastRegions)
_arrListOfBlastRegions
- ArrayList of feature Blast regionsprivate void setAllArguments(SimpleArg _allArguments)
_allArguments
- object which contains all command line argumentsprivate void setPredictions(java.util.ArrayList _predictions)
_predictions
- ArrayList of prediction objectsprivate void setGenePredicters(java.util.ArrayList _genePredicters)
_genePredicters
- ArrayList of genepredicter objectsprivate void setArrListOfGMRegions_org(java.util.ArrayList _arrListOfGMRegions_org)
_arrListOfGMRegions_org
- ArrayList of original genemodel regionsprivate void setAnalysisObjArr(java.util.ArrayList _analysisObjArr)
CDnaSpliceSiteAnalysis
, CDnaOverlapAnalysis
, BlastOverlapAnalysis
, TotalExonLengthAnalysis
, GeneModelLengthAnalysis
, AvgCondProbAnalysis
)
_analysisObjArr
- ArrayList of analysis objectsprivate void setMergedFeatureTableArr(java.util.ArrayList _mergedFeatureTableArr)
_mergedFeatureTableArr
- ArrayList of regions which contain high
scoring genemodels
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |